Bioconductors: We are pleased to announce Bioconductor 2.9, consisting of 517 software packages and more than 500 up-to-date annotation packages. There are 60 new software packages, and many updates and improvements to existing packages; 10 packages have been removed from this release. Bioconductor 2.9 is compatible with R 2.14.0, and is supported on Linux, 32- and 64-bit Windows, and Mac OS. This release includes an updated Bioconductor Amazon Machine Image. Visit http://bioconductor.org for details and downloads. Contents -------- * Getting Started with Bioconductor 2.9 * New Software Packages For the full release announcement, including package NEWS and a list of packages removed from the release, please visit the BioC 2.9 release page: http://bioconductor.org/news/bioc_2_9_release/ Getting Started with Bioconductor 2.9 ===================================== To install Bioconductor 2.9: 1. Install R 2.14.0. Bioconductor 2.9 has been designed expressly for this version of R. 2. Follow the instructions at http://bioconductor.org/install/. New Software Packages ===================== There are 60 new packages in this release of Bioconductor. - AGDEX: Agreement of Differential Expression Analysis - BiocInstaller: Install/Update Bioconductor and CRAN Packages - biovizBase: Basic graphic utilities for visualization of genomic data. - CellNOptR: R version of CellNOpt, boolean features only - CNAnorm: A normalization method for Copy Number Aberration in cancer samples. - cn.mops: Mixture of Poisson for CNV detection in NGS data - Cormotif: Correlation Motif Fit - cqn: Conditional quantile normalization - cummeRbund: cummeRbund: The finishing touch on your Tuxedo workflow. Analysis, exploration, manipulation, and visualization of Cufflinks HTS data. - DECIPHER: Database Enabled Code for Ideal Probe Hybridization Employing R - DEXSeq: Inference of differential exon usage in RNA-Seq - DiffBind: Differential Binding Analysis of ChIP-Seq peak data - dks: The double Kolmogorov-Smirnov package for evaluating multiple testing procedures. - DOSE: Disease Ontology Semantic and Enrichment analysis - DTA: Dynamic Transcriptome Analysis - EDASeq: Exploratory Data Analysis and Normalization for RNA-Seq - exomeCopy: Detection of CNV in exome/targeted sequencing data - fastseg: fastseg - a fast segmentation algorithm - flowType: Phenotyping Flow Cytometry Assays - flowWorkspace: Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore - GeneExpressionSignature: Gene Expression Signature based Similarity Metric - ggbio: Static visualization for genomic data. - GOFunction: GO-function: deriving biologcially relevant functions from statistically significant functions - graphite: GRAPH Interaction from pathway Topological Environment - GRENITS: Gene Regulatory Network Inference Using Time Series - GWASTools: GWASTools: Tools for Genome Wide Association Studies - htSeqTools: Quality Control, Visualization and Processing for High-Throughput Sequencing data - IdMappingRetrieval: ID Mapping Data Retrieval - inSilicoDb: Access to the InSilico Database - iontree: Data management and analysis of ion trees from ion-trap mass spectrometry - isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data - minfi: Analyze Illumina's 450k methylation arrays - MmPalateMiRNA: Murine Palate miRNA Expression Analysis - mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data) - ncdfFlow: ncdfFlow: A package that provides ncdf based storage based flow cytometry data. - NormqPCR: Functions for normalisation of RT-qPCR data - nucleR: Nucleosome positioning package for R - PAN: Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations - PREDA: Position RElated Data Anlysis - predictionet: Inference for predictive networks designed for (but not limited to) genomic data - qtbase: Interface between R and Qt - qtpaint: Qt-based painting infrastructure - r3Cseq: Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq) - RamiGO: AmiGO visualize R interface - randPack: Randomization routines for Clinical Trials - RCASPAR: A package for survival time prediction based on a piecewise baseline hazard Cox regression model. - ReadqPCR: Read qPCR data - RedeR: RedeR: bridging the gap between hierarchical network representation and functional analysis. - REDseq: Analysis of high-throughput sequencing data processed by restriction enzyme digestion - Repitools: Epigenomic tools - ReQON: Recalibrating Quality Of Nucleotides - rqubic: Qualitative biclustering algorithm for expression data analysis in R - RTopper: This package is designed to perform Gene Set Analysis across multiple genomic platforms - stepwiseCM: Stepwise Classification of Cancer Samples using Clinical and Molecular Data - Streamer: Enabling stream processing of large files - sva: Surrogate Variable Analysis - TSSi: Transcription Start Site Identification - tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family of distributions - VariantAnnotation: Annotation of Genetic Variants - zlibbioc: An R packaged zlib-1.2.5